GSR: Simulator - SIApopr

Basic Package Attributes
AttributeValue
Title SIApopr
Short Description Siapopr is an R package that wraps the C++ functions SIApop. These functions simulate birth-death-mutation processes with mutations having random fitnesses to simulate clonal evolution.
Long Description Siapopr is an R package that wraps the C++ functions SIApop. These functions simulate birth-death-mutation processes with mutations having random fitnesses to simulate clonal evolution.
Version Not available
Homepagehttps://github.com/olliemcdonald/siapopr#readme
Citations McDonald TO, Michor F, SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution., Bioinformatics, July 15, 2017 [ Abstract, cited in PMC ]
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluatedMay 17, 2022 (1068 days ago)
Author verificationThe basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataGenotype at Genetic Markers,
Variations
Simulation Method
Input
Data Type
File format
Output
Data Type
Sequencing Reads
File Format
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size Changes
Gene Flow
Spatiality
Life Cycle
Mating System
Fecundity
Natural Selection
DeterminantSingle-locus,
Models
Recombination
Mutation ModelsInfinite-allele Model, Others,
Events Allowed
Other
InterfaceCommand-line,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguageC or C++, R, Other,
LicenseOther,
GSR CertificationAccessibility, Documentation, Support,

Number of Primary Citations: 1

Number of Non-Primary Citations: 3

The following 3 publications are selected examples of applications that used SIApopr.

2019

Janiszewska M, Tabassum DP, Castaño Z, Cristea S, Yamamoto KN, Kingston NL, Murphy KC, Shu S, Harper NW, Del Alcazar CG, et al., Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments., Nat Cell Biol, July 1, 2019 [Abstract]

2018

McDonald TO, Chakrabarti S, Michor F, Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution., Nat Genet, Dec. 1, 2018 [Abstract]

Hinohara K, Wu HJ, Vigneau S, McDonald TO, Igarashi KJ, Yamamoto KN, Madsen T, Fassl A, Egri SB, Papanastasiou M, et al., KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance., Cancer Cell, Dec. 10, 2018 [Abstract]


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